#! /usr/bin/env guile
!#

(use-modules (srfi srfi-1)
             (srfi srfi-26)
             (ice-9 getopt-long)
             (ice-9 match)
             (ice-9 regex)
             (transform strings)
             (transform sql)
             (transform triples)
             (transform special-forms))


(define-transformer genelist
  (tables (GeneList
           (left-join Species "USING (SpeciesId)"))
          "GROUP BY BINARY GeneSymbol, GeneId, chromosome, txStart, txEnd")
  (schema-triples
   (gnt:gene rdfs:domain gnc:GeneSymbol)
   (gnt:belongsToSpecies rdfs:domain gnc:GeneSymbol)
   (gnc:GeneSymbol a rdfs:Class)
   (gnc:GeneSymbol rdfs:label "Gene Symbol")
   (gnc:transcript rdfs:domain gnc:GeneSymbol)
   (gnt:transcript a owl:ObjectProperty)
   (gnc:transcript rdfs:comments "The gene transcript of this resource")
   (gnc:hasKgID rdfs:domain gnc:GeneSymbol)
   (gnt:hasKgID a owl:ObjectProperty)
   (gnc:hasKgID rdfs:comments "The kgID of this resource")
   (gnc:hasUnigenID rdfs:domain gnc:GeneSymbol)
   (gnt:hasUnigenID a owl:ObjectProperty)
   (gnc:hasUnigenID rdfs:comments "The UnigenID of this resource")
   (gnc:hasProteinID rdfs:domain gnc:GeneSymbol)
   (gnt:hasProteinID a owl:ObjectProperty)
   (gnc:hasProteinID rdfs:comments "The ProteinID of this resource")
   (gnc:hasAlignID rdfs:domain gnc:GeneSymbol)
   (gnt:hasAlignID a owl:ObjectProperty)
   (gnc:hasAlignID rdfs:comments "The AlignID of this resource")
   (gnt:TxEnd rdfs:range xsd:double)
   (gnt:TxStart rdfs:range xsd:double)
   (gnt:hasTargetSeq rdfs:domain gnc:Probeset))
  (triples
      (string->identifier
       "gene" (regexp-substitute/global #f "[^A-Za-z0-9:]"
                                    (field GeneList GeneSymbol)
                                    'pre "_" 'post))
    (set rdf:type 'gnc:GeneSymbol)
    (set rdfs:label (field GeneList GeneSymbol))
    (set dct:description (sanitize-rdf-string (field GeneList GeneDescription)))
    (set gnt:gene (ontology 'gene: (field GeneList GeneId)))
    (set gnt:chromosome (field GeneList Chromosome))
    (set gnt:TxStart (annotate-field
                      (field GeneList TxStart)
                      '^^xsd:double))
    (set gnt:TxEnd (annotate-field
                    (field GeneList TxEnd)
                    '^^xsd:double))
    (set gnt:Strand (string-trim-both (field GeneList Strand)))
    (multiset
     gnt:belongsToSpecies
     (map
      (lambda (species)
        (string->identifier
         ""
         (remap-species-identifiers
          (string-trim-both species))
         #:separator ""
         #:proc string-capitalize-first))
      (string-split
       (sanitize-rdf-string
        (field ("GROUP_CONCAT( DISTINCT Species.Name )" SpeciesName)))
       #\,)))
    (multiset
     gnt:transcript
     (map
      (lambda (transcript)
        (ontology 'transcript:
                  (string-trim-both transcript)))
      (string-split
       (sanitize-rdf-string
        (field ("GROUP_CONCAT( DISTINCT NM_ID )" NMID)))
       #\,)))
    (multiset
     gnt:hasKgID
     (map string-trim-both
          (string-split
           (sanitize-rdf-string
            (field ("GROUP_CONCAT( DISTINCT kgID )" kgID)))
           #\,)))
    (multiset
     gnt:hasUnigenID
     (map string-trim-both
          (string-split
           (sanitize-rdf-string
            (field ("GROUP_CONCAT( DISTINCT UnigenID )" UnigenID)))
           #\,)))
    (multiset
     gnt:hasProteinID
     (map string-trim-both
          (string-split
           (sanitize-rdf-string
            (field ("GROUP_CONCAT( DISTINCT ProteinID )" ProteinID)))
           #\,)))
    (multiset
     gnt:hasAlignID
     (map string-trim-both
          (string-split
           (sanitize-rdf-string
            (field ("GROUP_CONCAT( DISTINCT AlignID )" AlignID)))
           #\,)))
    (multiset
     gnt:hasRgdID
     (map string-trim-both
          (string-split
           (sanitize-rdf-string
            (field ("GROUP_CONCAT( DISTINCT RGD_ID )" RgdID)))
           #\,)))))

(define-transformer genelist-rn33
  (tables (GeneList_rn33)
          "GROUP BY BINARY GeneSymbol, chromosome, txStart, txEnd")
  (triples
      (string->identifier
       "gene" (regexp-substitute/global #f "[^A-Za-z0-9:]"
                                    (field GeneList_rn33 geneSymbol)
                                    'pre "_" 'post))
    (set rdf:type 'gnc:GeneSymbol)
    (set rdfs:label (field GeneList_rn33 geneSymbol))
    (set gnt:chromosome (field GeneList_rn33 chromosome))
    (set gnt:TxStart (annotate-field
                      (field GeneList_rn33 txStart)
                      '^^xsd:double))
    (set gnt:TxEnd (annotate-field
                    (field GeneList_rn33 txEnd)
                    '^^xsd:double))
    (set gnt:Strand (string-trim-both (field GeneList_rn33 strand)))
    (set gnt:belongsToSpecies 'gn:Rattus_norvegicus)
    (multiset
     gnt:transcript
     (map
      (lambda (transcript)
        (ontology 'transcript:
                  (string-trim-both transcript)))
      (string-split
       (sanitize-rdf-string
        (field ("GROUP_CONCAT( DISTINCT NM_ID )" NMID)))
       #\,)))
    (multiset
     gnt:hasKgID
     (map string-trim-both
          (string-split
           (sanitize-rdf-string
            (field ("GROUP_CONCAT( DISTINCT kgID )" kgID)))
           #\,)))))



(let* ((option-spec
        '((settings (single-char #\s) (value #t))
          (output (single-char #\o) (value #t))
          (documentation (single-char #\d) (value #t))))
       (options (getopt-long (command-line) option-spec))
       (settings (option-ref options 'settings #f))
       (output (option-ref options 'output #f))
       (documentation (option-ref options 'documentation #f))
       (%connection-settings
        (call-with-input-file settings
          read)))
  (with-documentation
   (name "Gene Metadata")
   (connection %connection-settings)
   (table-metadata? #f)
   (prefixes
    '(("gn:" "<http://genenetwork.org/id/>")
      ("probeset:" "<http://genenetwork.org/probeset/>")
      ("gnc:" "<http://genenetwork.org/category/>")
      ("gnt:" "<http://genenetwork.org/term/>")
      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
      ("dct:" "<http://purl.org/dc/terms/>")
      ("owl:" "<http://www.w3.org/2002/07/owl#>")
      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
      ("qb:" "<http://purl.org/linked-data/cube#>")
      ("gene:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
      ("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
      ("transcript:" "<https://portals.broadinstitute.org/gpp/public/trans/details?transName=>")
      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
   (inputs
    (list genelist-rn33
          genelist))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))